If by "default save function" you mean the save built-in function, I'm confused by your later statement that "it pops a window for the user" since the save function does not show any window.
I suspect you want to bring up a dialog allowing the user to specify the file and directory in which to save the data then call save to save data in that location. In that case the uiputfile function may be of use to you. [As the Note on its documentation page states, uiputfile does not actually save the data, it just gives you a filename you can pass into save.]
If that's not what you're trying to do, please clarify with a bit more detail of what your end goal is.
